Their appears a common thread here - Windows 2000.
Microsoft have a section on Activesync problems and this can be found at
http://www.microsoft.com/windowsmobi...c/default.mspx
Two slightly offbeat comments in this hit me as being possible causes of upgrade problems.
1) Activesync and WM5 do not work well with hubs or laptop docking stations. The MS advise is to connect direct to the main machine.
2) This is just crazy enough the be the problem. Apparently activesync can sometimes see a USB WM5 connection as conflicting with a WiFi connection request and will disconnect this in favour of a network connection.
Try disabling your network connections and then upgrading the OS in Win2000. This problem is just crazy enough to cause the symptioms that people are seeing.